SARS-CoV-2-specific T-cell epitope repertoire in convalescent and mRNA-vaccinated individuals

Continuously emerging variants of concern (VOCs) sustain the SARS-CoV-2 pandemic. The SARS-CoV-2 Omicron/B.1.1.529 VOC harbours multiple mutations in the spike protein associated with high infectivity and efficient evasion from humoral immunity induced by previous infection or vaccination. By performing in-depth comparisons of the SARS-CoV-2-specific T-cell epitope repertoire after infection and messenger RNA vaccination, we demonstrate that spike-derived epitopes were not dominantly targeted in convalescent individuals compared to non-spike epitopes. In vaccinees, however, we detected a broader spike-specific T-cell response compared to convalescent individuals. Booster vaccination increased the breadth of the spike-specific T-cell response in convalescent individuals but not in vaccinees with complete initial vaccination. In convalescent individuals and vaccinees, the targeted T-cell epitopes were broadly conserved between wild-type SARS-CoV-2 variant B and Omicron/B.1.1.529. Hence, our data emphasize the relevance of vaccine-induced spike-specific CD8+ T-cell responses in combating VOCs including Omicron/B.1.1.529 and support the benefit of boosting convalescent individuals with mRNA vaccines.

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We look forward to hearing from you soon. {redacted} ******************* In the study SARS-CoV-2 specifc T cells induced by both SARS-CoV-2 infection and mRNA vaccination broadly cross-recognize omicron, Lang-Meli et al. Importantly, they also compare responses induced by natural infection vs vaccination down to the epitope level. This is of importance as it is still unclear if different or same epitopes are induced by either mechanism. The authors further address the question if there are differences in naturally infected then vaccinated compared to boosted vaccinees. Comments to the authors: • There is some concern as the authors for rely on previously identified CD8 T cells epitopes. It cannot be excluded that the authors would have identified novel CD8 epitopes in either vaccinated or naturally infection boosted vaccinees. Please add this limitation to the discussion. • It is not entirely clear how these selective sweep regions have been defined and how these 4 have been selected. Please add more detail to the methods section.
• Magnitude of T cell responses was compared after 10 days of stimulation. CD4 and CD8 T cells have very different kinetics of stimulation in vitro. While this should not affect the epitope specificity the reviewer doesn't think the authors can comment on the magnitude differences as shown in Figure 1F. Please consider deleting this.
Reviewer #2 (Remarks to the Author): In this manuscript, Lang-Meli and colleagues study the profile of T cells responding to both mRNA vaccination and previous infection. They demonstrate interesting changes in the specificities of responding T cells following either vaccination or infection and go one step further and study the responses following booster vaccination in both cases. They further demonstrate that these responses are able to cross-react to Omicron in many cases and that some are in conserved regions of spike that may therefore respond to any future arising variants. This is an interesting and well crafted study that will likely benefit the field as a whole.
One comment is that it seems like the responses presented in figure 2 are much less broad than what is presented in figure 1 and this isn't discussed. In addition, it appears that booster vaccination reduces the breadth of the CD4 T cell response but this isn't discussed in the manuscript. Both of these points should be clarified in the text.
Reviewer #3 (Remarks to the Author): Lang-Meli et al. describe in their manuscript SARS-CoV-2 T cell responses in convalescent and mRNAvaccinated individuals using (1) a panel of predescribed SARS-CoV-2 T cell epitopes and (2) whole spike protein overlapping peptide pools. They report that CD8 T cell responses targeting different spike peptides are lower in convalescent donors compared to vaccinees. For CD4+ T cells it was shown vise versa. Whereas the authors clearly demonstrate the differences in the T cell repertoire between convalescent and vaccinees, the data does not support the conclusion made by the authors in the title of the manuscript. T cell responses were all analyzed against the ancestral SARS-CoV-2 sequence and not against the omicron sequence. The statement that SARS-CoV-2-specific T cells cross-recognize omicron is not supported by this data. Furthermore, the authors suggest that the only relevant T cell responses are those against the spike protein, which indeed is not the case. A broad T cell response targeting multiple epitopes was shown to be most relevant to combat COVID-19. Intensity in terms of % of SARS-CoV-2 specific T cells in the two population was not assessed at all, which might be of central relevance to assess the quality of T cell response. Please find below the detailed comments on the manuscript and figures: -Of the 19 convalescent donors three were also vaccinated. Did the authors include samples of those donors before vaccination? Otherwise, these three should not be included in the cohort of convalescents and only used for the longitudinal analysis. -At which time point after vaccination or after infection were the blood samples collected? That should clearly be stated e.g. in Sup Table 1.
-The authors should provide a table with the 43 tested peptide sequences. In the method section, 60 peptides were described. Where does the difference between 43 and 60 come from? -Regarding the overlapping peptides: line 105: 180 peptides, method section line 29: 182 peptides, method section line 38: 181 peptides. What is the correct number? -Regarding the one spike-derived peptide affected by omicron (red in Figure 1A), a supplementary Figure or Table showing the sequence of the peptide and the sequence of the omicron variant would be helpful. Is it only affected by one amino acid? In which position? Anker position? The same could be analyzed for the affected peptides in Figure 1B and D. Why did the authors not test the convalescent and the vaccinated donors with the omicron peptides? Only by analyzing the T cell response against ancestral peptides AND omicron peptides can truly demonstrate if the T cells are able to recognize omicron sequences or if the T cell response in total is not reduced or affected by omicron.  Figure 1A: Are the frequency of donors who recognize a peptide normalized to the HLA allotypes? If not, why did 100% of convalescents recognize A*01-restricted peptides where only 6/19 convalescents are A*01 positive and why did 100% of the vaccinees recognize the A*03-restricted peptide where only 6/16 vaccinees are A*03 positive. How do the authors explain this? Figure 1B/D: Are the n numbers behind the HLA allotypes the number of donors with this allotype? One summary line per plot summarizing all donors independent of the allotype would be helpful. Figure 1F: For the convalescents CD4+ only 18 points are visible. That should be 19, shouldn't it? Regarding the statistics: A paired t test is not correct here since the donors of the different cohorts are not paired. I would suggest a nonparametric test such as the Mann-Whitney-Test.
-Did the authors test the donors of the vaccinee cohort for anti-nucleocapsid antibodies to be sure they did not have a previously unknown SARS-CoV-2 infection? -The data in the extended data Figure 1 does not match the statement in the text (line 112/113). The authors discuss the differences between convalescent and vaccinees and not the longitudinal analysis within the different cohorts, which is shown in the figure.
-Extended Data 1B: The different donors in these plots should be clearly labeled. The number of T cell responses depends on the HLA type of the donors hampering a comparison over all donors in the same plot.
-Using the terms cross-reactive and spike-specific together is very confusing and mutually exclusive (line 132/140). Cross-reactive peptides can be recognized by non-SARS-CoV-2-specific common cold coronavirus-primed T cells. The authors did not know if the vaccinees have cross-reactive T cells targeting the spike peptides before the vaccination. - Figure 2: Did the authors test the data for normality before using a t test? Maybe a nonparametric test such as Wilcoxon matched-pairs signed rank test would be better.
-The data about the sweep regions are not convincing since omicron showed 7 mutations in these regions.
-The extended data Figure 3 is not referred to in the text. For Pacific Blue the stained marker CD4 is not labeled on the axis. -Some typos: line 1: SARS-CoV-2-specific T cells, line 71: breakthrough, Supplementary

REFEREE #1:
In the study SARS-CoV-2 specific T cells induced by both SARS-CoV-2 infection and mRNA vaccination broadly cross-recognize omicron by Lang-Meli et al., importantly, they also compare responses induced by natural infection vs vaccination down to the epitope level. This is of importance as it is still unclear if different or same epitopes are induced by either mechanism. The authors further address the question if there are differences in naturally infected then vaccinated compared to boosted vaccinees.
We would like to thank this reviewer for the positive feedback and valuable comments regarding our study, especially with respect to acknowledging our comparative approach of identifying T cell responses down to the epitope level.
Comments to the authors: • There is some concern as the authors rely on previously identified CD8 T cells epitopes. It cannot be excluded that the authors would have identified novel CD8 epitopes in either vaccinated or naturally infection boosted vaccinees. Please add this limitation to the discussion.
We agree with this reviewer that with respect to the targeted epitope repertoire outside the spike protein, we completely rely on previously identified CD8+ T cell epitopes and thus neglect novel epitopes. However, to overcome the limitation of using pre-described epitopes with respect to spike-specific T cell responses, we additionally performed stimulation with overlapping peptides, followed by single-peptide intracellular cytokine read-out and in silico prediction of HLA restriction and optimal epitopes. Indeed, by using this approach, we detected substantially more CD8+ T cell responses targeting novel spike-specific T cell epitopes in vaccinees compared to convalescent donors ( Fig. 1B and Extended Data Fig. 1C+E).
• It is not entirely clear how these selective sweep regions have been defined and how these 4 have been selected. Please add more detail to the methods section.
We have now added more detailed information to the Methods section ( Subsequently to alignment with MAFFT, sweep regions were detected by using OmegaPlus and RAiSD, with the original SARS-CoV-2 isolate Wuhan-Hu-1 genome (NC_045512.2) as an outgroup. The common outliers were manually grouped into eight region of at least 50 bp, four of these were located in ORF1ab and four in the S region. Selective sweep 1 S323-434, selective sweep 2 S524-545, selective sweep 3 S888-S919, selective sweep 4 S965-S1,050 were identified by this method. VOC amino acid sequences were aligned to selective sweep regions; and peptides were mapped to the spike protein, to identify peptides that localize to the selective sweep regions.
• Magnitude of T cell responses was compared after 10 days of stimulation. CD4 and CD8 T cells have very different kinetics of stimulation in vitro. While this should not affect the epitope specificity the reviewer doesn't think the authors can comment on the magnitude differences as shown in Figure  1F. Please consider deleting this.
We appreciate the comment by the reviewer regarding previous Fig. 1F, now Extended Data Fig. 1E in the revised manuscript. We now mention the limited comparability of peptideexpansion of CD4+ versus CD8+ T cell responses on page 4, lines 113-115 of the revised manuscript. Since expansion procedures were, however, the same in vaccinees versus convalescents, the observed difference in the ratio between CD4+ and CD8+ T cell responses between these two groups may represent a biological relevant phenomenon.

REFEREE #2:
In this manuscript, Lang-Meli and colleagues study the profile of T cells responding to both mRNA vaccination and previous infection. They demonstrate interesting changes in the specificities of responding T cells following either vaccination or infection and go one step further and study the responses following booster vaccination in both cases. They further demonstrate that these responses are able to cross-react to Omicron in many cases and that some are in conserved regions of spike that may therefore respond to any future arising variants. This is an interesting and well-crafted study that will likely benefit the field as a whole.
We would like to thank this reviewer for acknowledging the strengths of our study and for the valuable remarks.
• One comment is that it seems like the responses presented in figure 2 are much less broad than what is presented in figure 1 and this isn't discussed.
In Fig. 1, the heatmaps depict a compilation of T cell responses from several donors whereas in Fig. 2, the heatmaps show the responses of one representative donor each. We have now better clarified this discrepancy in the respective figure legends. The median numbers of T cell responses per individual are, however, comparable (convalescents, CD4+: Fig. 1: 6 • In addition, it appears that booster vaccination reduces the breadth of the CD4 T cell response but this isn't discussed in the manuscript. Both of these points should be clarified in the text. In two of seven donors the numbers of detectable CD4+ T cell responses were reduced after 3 rd dose vaccination, in other two donors the numbers were increased and in three donors the numbers remained similar ( Fig. 2A, right panel; p>0.9). Hence, from these data, it cannot be concluded that the breadth of the CD4+ T cell response is reduced after the 3 rd dose vaccination. In the previous version of the manuscript, we indeed chose an 'exemplary' patient that did not well represent the overall results. We have now replaced the exemplary data by data from a more representative patient ( Fig. 2A, lower part).

REFEREE #3:
Lang-Meli et al. describe in their manuscript SARS-CoV-2 T cell responses in convalescent and mRNA-vaccinated individuals using (1) a panel of pre-described SARS-CoV-2 T cell epitopes and (2) whole spike protein overlapping peptide pools. They report that CD8 T cell responses targeting different spike peptides are lower in convalescent donors compared to vaccinees. For CD4+ T cells it was shown vice versa. Whereas the authors clearly demonstrate the differences in the T cell repertoire between convalescent and vaccinees, the data does not support the conclusion made by the authors in the title of the manuscript. T cell responses were all analyzed against the ancestral SARS-CoV-2 sequence and not against the omicron sequence. The statement that SARS-CoV-2-specific T cells cross-recognize omicron is not supported by this data. Furthermore, the authors suggest that the only relevant T cell responses are those against the spike protein, which indeed is not the case. A broad T cell response targeting multiple epitopes was shown to be most relevant to combat COVID-19. Intensity in terms of % of SARS-CoV-2 specific T cells in the two population was not assessed at all, which might be of central relevance to assess the quality of T cell response.
We would like to thank this reviewer for very thoroughly reviewing our manuscript and for the valuable comments that have helped to clarify and improve our manuscript. Indeed, the focus of this study was to dissect to what extent T cells either induced by mRNA vaccination (still including the ancestral spike sequence) or by natural infection (occurring in the pre-omicron period) cross-recognize omicron due to conservation of the targeted epitopes. This experimental approach is different but clearly complementary to the approach comparing overall T cell responses reactive against omicron or ancestral virus as suggested by reviewer #3. In the revised version of our manuscript, we have better clarified our experimental approach e.g. on page 2, lines 45-46 (abstract), page 4, lines 116-117, and page 5, lines 165-166. Hence, we believe that our main conclusion "Broad targeting of omicron by SARS-CoV-2-specific T cells after infection and vaccination" is supported by our experimental approach and relevantly complements the important findings gained by testing the overall cross-reactive T cell response towards SARS-CoV-2 omicron. An additional advantage of our approach is that our results can be easily transferred to newly emerging variants of concern (VOCs). Indeed, since the omicron subtype BA.2 already dominates the earlier omicron "prototype" BA.1 subtype in many countries, we have now extended our analysis to this subtype (see especially novel Extended Data Fig. 1B, Extended Data Fig. 4B, and Supplementary Table 3).
In addition, according to this reviewer's comment, we and others showed that a broad T cell response targeting epitopes in different viral proteins is associated with a mild course of COVID-19. As depicted in Figure 1A, our data confirm the broad targeting of multiple SARS-CoV-2 proteins in convalescents. We have more strongly emphasized this point in the revised version of the manuscript (page 2/3, lines 67-69). In this study, we analyzed the spike-specific T cell epitope repertoire after mRNA vaccination compared to natural infection in more detail and our conclusions concerning the comprehensively analyzed repertoire of the T cell response are indeed limited to the spike protein. We have clarified this point throughout the revised manuscript.
As suggested by this reviewer, we have added the comparison of the intensity of T cell responses (indicated as %IFN-gamma producing T cells) in the two groups as Extended data Fig. 1A to the revised manuscript. These data again highlight the important role of non-spike epitopes in resolved SARS-CoV-2 infection.
Please find below the detailed comments on the manuscript and figures: -Of the 19 convalescent donors three were also vaccinated. Did the authors include samples of those donors before vaccination? Otherwise, these three should not be included in the cohort of convalescents and only used for the longitudinal analysis.
In the analysis of the cohort of 19 convalescent donors (e.g., Fig. 1 and associated Extended Data Fig. 1), we included pre-vaccination samples of these three donors. Samples after vaccination of these three patients, however, were included in Fig. 2B and Extended Data Fig.  3B. These figure panels also contain a timeline of sampling in these three patients. Following the next comment by the reviewer, we have now also included the exact sampling time points in Supplementary Table 1. This will definitively help to clarify the important issue of timing of sampling, and we apologize for any ambiguity in the previous version of our manuscript.
-At which time point after vaccination or after infection were the blood samples collected? That should clearly be stated e.g. in Sup Table 1.
The time points were added accordingly in Supplementary Table 1. -The authors should provide a table with the 43 tested peptide sequences. In the method section, 60 peptides were described. Where does the difference between 43 and 60 come from?
We now provide a Table with the peptide sequences as requested (Supplementary Table 2). The document can also be found on the public repository "Open Science Framework" via https://osf.io/zbk6q/ . Of note, we tested a total of 60 peptides, but included only those 43 peptides in the analysis (e.g., Fig. 1A) that were tested in a minimum of 3 patients with the corresponding HLA type for statistical reasons. We apologize for this ambiguity in the previous version of our manuscript and now explain this selection strategy in the methods section (page 7, lines 207-210 of the revised manuscript).
-Regarding the overlapping peptides: line 105: 180 peptides, method section line 29: 182 peptides, method section line 38: 181 peptides. What is the correct number? 1 We apologize for this inconsistency in the previous version of the manuscript. We designed the set of overlapping peptides to include 180 peptides with the ancestral virus sequences plus 2 peptides containing the 2 amino acid substitutions present in the "stabilized" mRNA vaccine sequence. We now explain the design and number of overlapping peptides on page 7, lines 204-207 of the revised manuscript and use the number of 182 overlapping peptides throughout the manuscript.
-Regarding the one spike-derived peptide affected by omicron (red in Figure 1A), a supplementary Figure or Table showing the sequence of the peptide and the sequence of the omicron variant would be helpful. Is it only affected by one amino acid? In which position? Anker position? The same could be analyzed for the affected peptides in Figure 1B and D. Table 3, taking into account the omicron subtypes BA.1 and BA.2.

This important information is now displayed in Supplementary
-Why did the authors not test the convalescent and the vaccinated donors with the omicron peptides? Only by analyzing the T cell response against ancestral peptides AND omicron peptides can truly demonstrate if the T cells are able to recognize omicron sequences or if the T cell response in total is not reduced or affected by omicron.
As mentioned above, we completely agree with this reviewer about the relevance to test the omicron-reactive T cell response to address whether the T cell response in total is affected by omicron. Our approach is complementary, focusing on the identification of T cell responses elicited by ancestral spike sequences in mRNA vaccination compared to natural infection in the pre-omicron times down to the epitope level. Hence, we do not measure cross-reactive but rather cross-recognizing T cell responses towards omicron. We have thoroughly used the term "cross-recognizing" in the revised manuscript. The Figures are now labeled accordingly to clarify which cohort is depicted. In Fig. 1, only vaccinees after the second dose were analyzed, and this is now clearly stated in the legend. The abbreviations NTD, RBD, and FCS as well as the exact terminology of wt versus mut are now explained in the legend to Fig. 1. - Figure 1A: Are the frequency of donors who recognize a peptide normalized to the HLA allotypes? If not, why did 100% of convalescents recognize A*01-restricted peptides where only 6/19 convalescents are A*01 positive and why did 100% of the vaccinees recognize the A*03-restricted peptide where only 6/16 vaccinees are A*03 positive. How do the authors explain this?
The frequency of donors who recognize a peptide is indeed normalized to the HLA allotypes. This is now explained in the legend to Fig. 1A.
- Figure 1B/D: Are the n numbers behind the HLA allotypes the number of donors with this allotype? One summary line per plot summarizing all donors independent of the allotype would be helpful.
Indeed, the numbers indicate the number of individuals with the respective HLA allotype. This is now stated in the legend to Fig. 1B. We have added a summary line per plot summarizing all donors as suggested.
- Figure 1F: For the convalescents CD4+ only 18 points are visible. That should be 19, shouldn't it? Regarding the statistics: A paired t test is not correct here since the donors of the different cohorts are not paired. I would suggest a nonparametric test such as the Mann-Whitney-Test.
We apologize for the missing data point in previous Fig. 1F, now Extended Data Fig. 1E. We have now included the missing data. In addition, we have used the nonparametric Mann-Whitney-Test as suggested in the revised version (Extended Data Fig. 1E).
-Did the authors test the donors of the vaccinee cohort for anti-nucleocapsid antibodies to be sure they did not have a previously unknown SARS-CoV-2 infection?
The vaccinees were now tested for anti-nucleocapsid antibodies to exclude a previously unknown SARS-CoV-2 infection. This important information is now stated on page 6, lines 184-185 of the methods section.
-The data in the extended data Figure 1 does not match the statement in the text (line 112/113). The authors discuss the differences between convalescent and vaccinees and not the longitudinal analysis within the different cohorts, which is shown in the figure.
We agree with the reviewer that the longitudinal analysis was not mentioned at the best suited text paragraph. We now mention the stable T cell epitope repertoire observed in the longitudinal analysis (now Extended Data Fig. 2) on page 4, lines 106-108.
-Extended Data 1B: The different donors in these plots should be clearly labeled. The number of T cell responses depends on the HLA type of the donors hampering a comparison over all donors in the same plot.
In previous Extended Data Fig. 1B (now Extended Data Fig. 2B), the number of targeted overlapping peptides is indicated, irrespective of HLA type of the individual. All 19 convalescents are included in this analysis, and this is now clearly stated in the figure legend.
-Using the terms cross-reactive and spike-specific together is very confusing and mutually exclusive (line 132/140). Cross-reactive peptides can be recognized by non-SARS-CoV-2-specific common cold coronavirus-primed T cells. The authors did not know if the vaccinees have cross-reactive T cells targeting the spike peptides before the vaccination.
We have removed the ambiguous term cross-reactive throughout the manuscript.
- Figure 2: Did the authors test the data for normality before using a t test? Maybe a nonparametric test such as Wilcoxon matched-pairs signed rank test would be better.
We have now used the nonparametric Wilcoxon matched-pairs signed rank test in the revised version of Fig. 2. -The data about the sweep regions are not convincing since omicron showed 7 mutations in these regions.
As also pointed out in the reply to reviewer #1, selective sweep regions were defined according to Kang et al. (Kang L, He G, Sharp AK, et al. A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Cell 2021;184:4392-400). In brief, Kang et al. analyzed total of 136,114 complete SARS-CoV-2 genomes from the human host. Subsequently to alignment with MAFFT, sweep regions were detected by using OmegaPlus and RAiSD, with the original SARS-CoV-2 isolate Wuhan-Hu-1 genome (NC_045512.2) as an outgroup. The common outliers were manually grouped into eight regions of at least 50 bp, four of these were located in ORF1ab and four in the S region. Selective sweep 1 S323-434, selective sweep 2 S524-545, selective sweep 3 S888-S919, selective sweep 4 S965-S1,050 were identified by this method. VOC were aligned to these selective sweep regions and peptides were mapped to the spike protein, to identify peptides that localize to the selective sweep regions identified by Kang et al.. Hence, selective sweep regions were not only defined based on the currently circulating VOC but more broadly cover SARS-CoV-2 genomes. We have extended the information about the definition of the selective sweep regions in the Methods section (page 8, lines 253-263 of the revised manuscript) and now more clearly state that the selective sweep regions are affected by point mutations in omicron (page 5, lines 145-147 of the revised manuscript).
-The extended data Figure 3 is not referred to in the text. For Pacific Blue the stained marker CD4 is not labeled on the axis.  We have corrected the typos in the revised version of the manuscript.
- Supplementary Table 1: List of abbreviations is missing. Mild defines the course of COVID-19 not the natural infection.
We have added a list of abbreviations and have changed the title of the respective column in Supplementary Table 1 from "Natural infection" to "Severity of COVID-19"

Decision Letter, first revision:
Dear Maike, Thank you for submitting your revised manuscript "Broad targeting of omicron by SARS-CoV-2-specific T cells after infection and vaccination" (NMICROBIOL-22010115A). It has now been seen by the original referees and their comments are below. The reviewers find that the paper has improved in revision, and therefore we'll be happy in principle to publish it in Nature Microbiology, pending minor revisions to satisfy the referees' final requests and to comply with our editorial and formatting guidelines. In addition, just to let you know, we have changed the article type for the submission to Article as this will give you more space to include all required data, information and references as compared to a Brief Communication.
If the current version of your manuscript is in a PDF format, please email us a copy of the file in an editable format (Microsoft Word or LaTex)--we can not proceed with PDFs at this stage.
We are now performing detailed checks on your paper and will send you a checklist detailing our editorial and formatting requirements in about a week. Please do not upload the final materials and make any revisions until you receive this additional information from us. The authors have implemented the suggestions well and significantly improved the quality of the manuscript. However, the title of the manuscript is still not reflecting the performed experiments and received results! The title should be changed and not include omicron! The following small errors have been noticed: -Supplementary Table 3: "Small IC50/low rank": The authors should better explain what the cutoff values are for strong, weak and no binders. - Figure 1B: the n numbers of convalescents and vaccinees are interchanged in the CD8 plots. In the Figure legend the authors should add "to overlapping peptides of the spike protein" - Figure 2A and B: The wt legend is not clearly labeled.

Decision Letter, final checks:
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Please note that <i>Nature Microbiology</i> is a Transformative Journal (TJ). Authors may publish their research with us through the traditional subscription access route or make their paper immediately open access through payment of an article-processing charge (APC). Authors will not be required to make a final decision about access to their article until it has been accepted. <a href="https://www.springernature.com/gp/open-research/transformative-journals"> Find out more about Transformative Journals</a> Authors may need to take specific actions to achieve <a href="https://www.springernature.com/gp/open-research/funding/policy-compliancefaqs"> compliance</a> with funder and institutional open access mandates. If your research is supported by a funder that requires immediate open access (e.g. according to <a href="https://www.springernature.com/gp/open-research/plan-s-compliance">Plan S principles</a>) then you should select the gold OA route, and we will direct you to the compliant route where possible. For authors selecting the subscription publication route, the journal's standard licensing terms will need to be accepted, including <a href="https://www.springernature.com/gp/openresearch/policies/journal-policies">self-archiving policies</a>. Those licensing terms will supersede any other terms that the author or any third party may assert apply to any version of the manuscript. The authors have implemented the suggestions well and significantly improved the quality of the manuscript. However, the title of the manuscript is still not reflecting the performed experiments and received results! The title should be changed and not include omicron! The following small errors have been noticed: -Supplementary Table 3: "Small IC50/low rank": The authors should better explain what the cutoff values are for strong, weak and no binders. - Figure 1B: the n numbers of convalescents and vaccinees are interchanged in the CD8 plots. In the Figure legend the authors should add "to overlapping peptides of the spike protein" - Figure 2A and B: The wt legend is not clearly labeled.

Final Decision Letter:
Dear Maike, I am pleased to accept your Article "SARS-CoV-2-specific T cell epitope repertoire in convalescent and mRNA-vaccinated individuals" for publication in Nature Microbiology. Thank you for having chosen to submit your work to us and many congratulations.
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Please note that <i>Nature Microbiology</i> is a Transformative Journal (TJ). Authors may publish their research with us through the traditional subscription access route or make their paper immediately open access through payment of an article-processing charge (APC). Authors will not be required to make a final decision about access to their article until it has been accepted. <a href="https://www.springernature.com/gp/open-research/transformative-journals"> Find out more about Transformative Journals</a> Authors may need to take specific actions to achieve <a href="https://www.springernature.com/gp/open-research/funding/policy-compliancefaqs"> compliance</a> with funder and institutional open access mandates. If your research is supported by a funder that requires immediate open access (e.g. according to <a href="https://www.springernature.com/gp/open-research/plan-s-compliance">Plan S principles</a>) then you should select the gold OA route, and we will direct you to the compliant route where possible. For authors selecting the subscription publication route, the journal's standard licensing terms will need to be accepted, including <a href="https://www.springernature.com/gp/openresearch/policies/journal-policies">self-archiving policies</a>. Those licensing terms will supersede any other terms that the author or any third party may assert apply to any version of the manuscript.
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